Tree Building (imported from uploaded file)

evolution-abc_intro_phylo/tree-building

Author(s)
Helena Rasche, Michael Charleston
Version
1
Last updated
May 10, 2024
License
MIT
Tags
evolution

Features
Tutorial
Phylogenetics - Back to basics
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00072
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nInput FASTA Sequence File"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["MAFFT"];
  0 -->|output| 1;
  e5d56101-daff-420b-82e9-dc6cc923f7ab["Output\noutputAlignment"];
  1 --> e5d56101-daff-420b-82e9-dc6cc923f7ab;
  style e5d56101-daff-420b-82e9-dc6cc923f7ab stroke:#2c3143,stroke-width:4px;
  2["FASTTREE"];
  1 -->|outputAlignment| 2;
  632ce28d-3086-490e-bd97-949eb2cb385a["Output\noutput"];
  2 --> 632ce28d-3086-490e-bd97-949eb2cb385a;
  style 632ce28d-3086-490e-bd97-949eb2cb385a stroke:#2c3143,stroke-width:4px;
  3["IQ-TREE"];
  1 -->|outputAlignment| 3;
  b8434b2b-2001-4b1a-bd06-faeab18519a4["Output\ntreefile"];
  3 --> b8434b2b-2001-4b1a-bd06-faeab18519a4;
  style b8434b2b-2001-4b1a-bd06-faeab18519a4 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Input FASTA Sequence File

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.508+galaxy1 MAFFT
toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1 FASTTREE
toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.1.2+galaxy2 IQ-TREE

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.1.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.508+galaxy1 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
3 b66d2fb9e 2024-04-23 00:49:00 Update tree-building.ga
2 04d8111aa 2024-04-22 07:48:07 fix workflow loading, slide linting
1 7fa178fb3 2024-03-18 10:31:04 Add workflow which matches tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/evolution/tutorials/abc_intro_phylo/workflows/tree-building.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows